Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Conserved Binding Sites01:49

Conserved Binding Sites

5.0K
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
5.0K
Conserved Binding Sites01:49

Conserved Binding Sites

1.9K
1.9K
Ligand Binding Sites02:40

Ligand Binding Sites

14.7K
Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
14.7K
Ligand Binding Sites02:40

Ligand Binding Sites

8.5K
8.5K
Protein-protein Interfaces02:04

Protein-protein Interfaces

14.4K
Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
14.4K
Protein-Drug Binding: Mechanism and Kinetics01:16

Protein-Drug Binding: Mechanism and Kinetics

1.5K
Protein-drug binding refers to the interaction between drugs and proteins within the body. This binding process can occur intracellularly, involving drug interactions with enzymes or receptors within cells, or extracellularly, involving plasma proteins in the blood.
Various forces drive these interactions, including hydrogen bonds, hydrophobic interactions, ionic bonds, electrostatic interactions, and van der Waals forces. These bonds enable drugs to bind to specific sites on proteins,...
1.5K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Prediction of antibody non-specificity using protein language models and biophysical parameters.

mAbs·2026
Same author

<i>In vitro</i> and <i>in vivo</i> inhibition of amyloid β aggregation by a Ru(II)-naphthalene diimide complex.

Dalton transactions (Cambridge, England : 2003)·2026
Same author

Comparative Transcriptomic Analysis of Two Apple Cultivars in Response to Dual Cytokinin Applied In Vitro.

Plants (Basel, Switzerland)·2026
Same author

Herpes simplex virus type 1 R-loops are targets for APOBEC-mediated mutagenesis.

Genome biology·2026
Same author

Rapid elongation drives the exceptionally fast aggregation of the most common localized human amyloid medin.

Communications chemistry·2026
Same author

Systems-level organization of extracellular proteostasis.

Science (New York, N.Y.)·2026

Related Experiment Video

Updated: Dec 20, 2025

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
06:50

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

2.4K

Sequence-based prediction of protein binding mode landscapes.

Attila Horvath1,2, Marton Miskei1, Viktor Ambrus1

  • 1MTA-DE Laboratory of Protein Dynamics, Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen, Hungary.

Plos Computational Biology
|May 27, 2020
PubMed
Summary

Researchers developed FuzPred, an algorithm predicting how intrinsically disordered proteins bind partners. This method analyzes amino acid sequences to determine context-dependent binding modes, crucial for understanding cellular regulation.

More Related Videos

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

69.6K
Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

17.5K

Related Experiment Videos

Last Updated: Dec 20, 2025

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
06:50

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

2.4K
A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

69.6K
Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

17.5K

Area of Science:

  • Protein intrinsically disordered regions
  • Biophysics of protein-protein interactions
  • Computational biology

Background:

  • Disordered proteins exhibit dynamic conformational ensembles.
  • Protein-partner interactions can involve disorder-to-order (DO) or disorder-to-disorder (DD) transitions.
  • Some proteins display context-dependent binding modes, termed 'fuzzy' binding.

Purpose of the Study:

  • Investigate the amino acid determinants of fuzzy binding.
  • Develop a computational method to predict context-dependent binding modes from amino acid sequences.
  • Identify regulatory sites sensitive to cellular context or post-translational modifications.

Main Methods:

  • Quantified fuzzy binding using entropy of transitions towards decreasing order.
  • Integrated entropy calculations into the FuzPred algorithm.
  • Validated FuzPred predictions using diverse protein examples.

Main Results:

  • FuzPred successfully predicts the range of binding modes for fuzzy proteins.
  • The algorithm identifies amino acid sequences associated with context-dependent binding.
  • Identified binding sites are sensitive to cellular context and post-translational modifications.

Conclusions:

  • Amino acid sequence encodes information for fuzzy binding.
  • FuzPred provides a valuable tool for predicting protein binding versatility.
  • This approach can reveal regulatory mechanisms in cellular pathways.